WASHINGTON — Facing a backlash over long security lines and management problems, the head of the Transportation Security Administration shook up his leadership team on Monday, replacing the agency’s top security official and adding a new group of administrators at Chicago O’Hare International Airport.

In an email to staff members, Peter V. Neffenger, the TSA administrator, announced a series of changes that included the removal of Kelly Hoggan, who had been the assistant administrator for the Office of Security Operations since 2013.

Beginning late that year, Hoggan received $90,000 in bonuses over a 13-month period, even though a leaked report from the Department of Homeland Security showed that auditors were able to get fake weapons and explosives past security screeners 95 percent of the time in 70 covert tests.

In addition, several employees who say they were punished with reassignments to other airports after filing whistleblower complaints have alleged that Hoggan played a role in their forced transfers.

Hoggan’s bonus was paid out in $10,000 increments, an arrangement that members of Congress have said was intended to disguise the payments. During a hearing of the House Oversight Committee two weeks ago, lawmakers grilled Neffenger about the bonus, which was issued before he joined the agency in July.

“Those bonuses were given to somebody who oversees a part of the operation that was in total failure,” said Rep. Jason Chaffetz, R-Utah, the committee’s chairman.

Neffenger said he had changed the rules to cap bonuses at $10,000 a year.

Asked during the hearing if he would discipline or remove Hoggan, Neffenger said he would not, adding that he had no evidence of any wrongdoing. But by Monday, he appeared to have had a change of heart.

Neffenger announced that Darby LaJoye, a deputy assistant administrator at the agency, would immediately take over as acting assistant administrator of the Office of Security Operations. LaJoye will manage security operations for the agency’s workforce of more than 50,000 employees at about 440 airports nationwide.

Several current and former TSA employees said the moves to replace Hoggan and add the new officials in Chicago, where passengers have endured hourslong waits at security checkpoints, were insufficient.

“The timing of this decision is too late to make a real difference for the summer,” said Andrew Rhoades, an assistant federal security director at Minneapolis-St. Paul International Airport. “Neffenger is only doing this because the media and Congress are making him look bad.”

Rhoades has filed a whistleblower complaint against the agency. Later, he said, he was ordered to racially profile Somali-Americans visiting the TSA’s local office.

“No one thinks he is really making any meaningful changes,” said Livingston, who has sued the agency, claiming he was demoted because he reported misconduct by senior managers. “Bottom line is no one in TSA believes in Neffenger now. He is only acting out of desperation.”

In the changes in Chicago, Neffenger announced that a new TSA leadership team was now overseeing screening operations at O’Hare Airport, which has had some of the longest waiting times of any airport in the country.

On Sunday, hundreds of passengers, including 450 on American Airlines alone, missed flights because of waits of two or three hours in security lines, according to local news reports. Many of the passengers had to spend the night in the terminal sleeping on cots.

The TSA has sent 58 additional security officers and four more bomb-sniffing dog teams to O’Hare. Last week, Neffenger apologized to passengers and briefed officials in Chicago about efforts to address the crushing delays.

The agency has attributed the lines, in part, to tightened security procedures and budget cuts that have caused a shortage of screeners.

In his email to the agency’s staff, Neffenger also announced the creation of an Incident Command Center at the agency’s headquarters. The center will closely track daily screening operations, shifting officers and bomb-sniffing dogs to better allocate the agency’s resources.

“These adjustments will enable more focused leadership and screening operations at critical airports in the national transportation system,” Neffenger wrote.